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1. Detecting population declines via monitoring the effective number of breeders ( N _b )

   https://doi.org/10.1111/1755-0998.13251  

   Luikart, Gordon; Antao, Tiago; Hand, Brian K.; Muhlfeld, Clint C.; Boyer, Matthew C.; Cosart, Ted; Trethewey, Brian; Al‐Chockhachy, Robert; Waples, Robin S. (January 2020, Molecular Ecology Resources)

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2. Ancient DNA and deep population structure in sub-Saharan African foragers

   https://doi.org/10.1038/s41586-022-04430-9  

   Lipson, Mark; Sawchuk, Elizabeth A.; Thompson, Jessica C.; Oppenheimer, Jonas; Tryon, Christian A.; Ranhorn, Kathryn L.; de Luna, Kathryn M.; Sirak, Kendra A.; Olalde, Iñigo; Ambrose, Stanley H.; et al (March 2022, Nature)

   Abstract Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa 1–4 . Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations 3,5 . Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80–20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch. 

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3. Estimating spread of contact-based contagions in a population through sub-sampling

   https://doi.org/10.14778/3461535.3461544  

   Zeighami, Sepanta; Shahabi, Cyrus; Krumm, John (May 2021, Proceedings of the VLDB Endowment)

   Various phenomena such as viruses, gossips, and physical objects (e.g., packages and marketing pamphlets) can be spread through physical contacts. The spread depends on how people move, i.e., their mobility patterns. In practice, mobility patterns of an entire population is never available, and we usually have access to location data of a subset of individuals. In this paper, we formalize and study the problem of estimating the spread of a phenomena in a population, given that we only have access to sub-samples of location visits of some individuals in the population. We show that simple solutions that estimate the spread in the sub-sample and scale it to the population, or more sophisticated solutions that rely on modeling location visits of individuals do not perform well in practice. Instead, we directly model the co-locations between the individuals. We introduce PollSpreader and PollSusceptible, two novel approaches that model the co-locations between individuals using a contact network , and infer the properties of the contact network using the sub-sample to estimate the spread of the phenomena in the entire population. We analytically show that our estimates provide an upper bound and a lower bound on the spread of the disease in expectation. Finally, using a large high-resolution real-world mobility dataset, we experimentally show that our estimates are accurate in practice, while other methods that do not correctly account for co-locations between individuals result in entirely wrong observations (e.g, premature prediction of herd-immunity). 

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4. Mind the GAP: Improving Robustness to Sub-population Shifts with Group-Aware Priors.

   Rudner, Tim G; Zhang, Ya S; Wilson, Andrew G; Kempe, J (May 2024, Artificial Intelligence and Statistics)

   Machine learning models often perform poorly under subpopulation shifts in the data distribution. Developing methods that allow machine learning models to better generalize to such shifts is crucial for safe deployment in real-world settings. In this paper, we develop a family of group-aware prior (GAP) distributions over neural network parameters that explicitly favor models that generalize well under subpopulation shifts. We design a simple group-aware prior that only requires access to a small set of data with group information and demonstrate that training with this prior yields state-of-the-art performance -- even when only retraining the final layer of a previously trained non-robust model. Group aware-priors are conceptually simple, complementary to existing approaches, such as attribute pseudo labeling and data reweighting, and open up promising new avenues for harnessing Bayesian inference to enable robustness to subpopulation shifts. 

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5. Unveiling the population of dual and lensed active galactic nuclei at sub-arcsec separations

   https://doi.org/10.1038/s41550-022-01761-5  

   Mannucci, F.; Pancino, E.; Belfiore, F.; Cicone, C.; Ciurlo, A.; Cresci, G.; Lusso, E.; Marasco, A.; Marconi, A.; Nardini, E.; et al (October 2022, Nature Astronomy)